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- PDB-4xcm: Crystal structure of the putative NlpC/P60 D,L endopeptidase from... -

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Basic information

Entry
Database: PDB / ID: 4xcm
TitleCrystal structure of the putative NlpC/P60 D,L endopeptidase from T. thermophilus
ComponentsCell wall-binding endopeptidase-related protein
KeywordsHYDROLASE / NlpC/P60 / D / L-endopeptidase / LysM domain
Function / homology
Function and homology information


Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Lysin motif / LysM domain superfamily / LysM domain ...Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Papain-like cysteine peptidase superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Cell wall-binding endopeptidase-related protein
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsWong, J. / Midtgaard, S. / Gysel, K. / Thygesen, M.B. / Sorensen, K.K. / Jensen, K.J. / Stougaard, J. / Thirup, S. / Blaise, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase.
Authors: Wong, J.E. / Midtgaard, S.R. / Gysel, K. / Thygesen, M.B. / Srensen, K.K. / Jensen, K.J. / Stougaard, J. / Thirup, S. / Blaise, M.
History
DepositionDec 18, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Jul 20, 2016Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell wall-binding endopeptidase-related protein
B: Cell wall-binding endopeptidase-related protein


Theoretical massNumber of molelcules
Total (without water)53,3802
Polymers53,3802
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-29 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.600, 71.600, 197.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Cell wall-binding endopeptidase-related protein


Mass: 26689.967 Da / Num. of mol.: 2 / Fragment: UNP residues 15-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA0266 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): rosetta2 / References: UniProt: Q5SLM7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium citrate pH 5.5, 16% PEG 4000, 15% 2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 34882 / Num. obs: 34817 / % possible obs: 99.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.3
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→29.584 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2383 3316 10.09 %
Rwork0.1941 --
obs0.1986 32875 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→29.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3056 0 0 16 3072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033134
X-RAY DIFFRACTIONf_angle_d0.7064262
X-RAY DIFFRACTIONf_dihedral_angle_d13.631169
X-RAY DIFFRACTIONf_chiral_restr0.044470
X-RAY DIFFRACTIONf_plane_restr0.004555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6501-2.6880.32691360.3051252X-RAY DIFFRACTION100
2.688-2.72811261191X-RAY DIFFRACTION100
2.7281-2.77070.33511460.26341230X-RAY DIFFRACTION100
2.7707-2.8160.34431400.25921252X-RAY DIFFRACTION100
2.816-2.86460.35631400.27271289X-RAY DIFFRACTION100
2.8646-2.91660.33051220.27921185X-RAY DIFFRACTION100
2.9166-2.97270.37821480.25431234X-RAY DIFFRACTION100
2.9727-3.03330.29541440.24761209X-RAY DIFFRACTION100
3.0333-3.09920.31491330.24821271X-RAY DIFFRACTION100
3.0992-3.17120.35571400.23381196X-RAY DIFFRACTION100
3.1712-3.25040.2991440.23031281X-RAY DIFFRACTION100
3.2504-3.33820.29421280.2361185X-RAY DIFFRACTION100
3.3382-3.43620.25111420.20811254X-RAY DIFFRACTION100
3.4362-3.5470.30391340.21951221X-RAY DIFFRACTION100
3.547-3.67350.27141380.19961197X-RAY DIFFRACTION100
3.6735-3.82030.26721520.1981274X-RAY DIFFRACTION100
3.8203-3.99380.21151400.18831230X-RAY DIFFRACTION100
3.9938-4.20380.23941360.17161248X-RAY DIFFRACTION100
4.2038-4.46630.18491400.16491225X-RAY DIFFRACTION100
4.4663-4.80980.16911380.13921229X-RAY DIFFRACTION100
4.8098-5.29140.18971410.14511217X-RAY DIFFRACTION100
5.2914-6.05140.18341280.18281234X-RAY DIFFRACTION100
6.0514-7.60260.2231320.18241247X-RAY DIFFRACTION100
7.6026-29.58580.19321480.17471208X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.41543.41565.02449.19435.435410.12690.8270.0872-1.24411.172-0.1427-0.42241.4915-0.3203-0.63340.8095-0.2029-0.08690.7224-0.11810.7158-51.0697-17.6172-4.5884
20.7722.70420.7397.2370.09954.8408-1.09911.36640.8295-0.61380.60090.6116-0.69390.3590.21861.1366-0.2299-0.2660.85960.01280.9546-47.6647-2.8125-8.5911
38.04823.9166-0.765410.7082-1.16685.5867-0.00460.2940.5765-0.0072-0.109-0.0167-0.35170.22630.03830.6009-0.08140.05160.42510.09530.4631-35.584614.23113.2161
44.9333-1.9155-2.13954.6588-0.12521.3345-0.18980.3145-0.7377-0.2508-0.1363-2.394-0.08561.0530.28760.627-0.17050.10861.08280.1481.5946-14.184518.0453-1.8182
54.5854-1.4484-2.10594.855-3.624310.0344-0.03960.5350.004-0.62420.20350.03220.92540.0486-0.05711.4020.2488-0.19211.7125-0.12931.13314.50821.854510.5412
68.85567.17121.27174.60221.315-0.3237-1.51161.7405-0.5566-0.92241.6769-0.5235-0.83560.389-0.12361.36180.0563-0.08311.2877-0.12131.1991-9.18369.47284.6206
77.92493.76465.18316.15231.70378.73670.6484-0.1666-1.03640.6568-0.0824-0.24871.8208-0.1014-0.48411.0215-0.0175-0.04770.3704-0.0140.4562-39.1509-10.43279.2544
88.7872-3.8872-0.34116.55140.0123.16070.4896-0.1547-0.47990.8819-0.2168-0.5740.8790.2116-0.15271.08290.0553-0.20930.51530.02360.4821-32.6277-6.551718.3077
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 246 )
4X-RAY DIFFRACTION4chain 'B' and (resid 17 through 64 )
5X-RAY DIFFRACTION5chain 'B' and (resid 65 through 104 )
6X-RAY DIFFRACTION6chain 'B' and (resid 105 through 129 )
7X-RAY DIFFRACTION7chain 'B' and (resid 130 through 228 )
8X-RAY DIFFRACTION8chain 'B' and (resid 229 through 245 )

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